<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
<!--NewPage-->
<HTML>
<HEAD>
<TITLE>
MutationMention (snp-normalizer)
</TITLE>


<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">

<SCRIPT type="text/javascript">
function windowTitle()
{
    if (location.href.indexOf('is-external=true') == -1) {
        parent.document.title="MutationMention (snp-normalizer)";
    }
}
</SCRIPT>
<NOSCRIPT>
</NOSCRIPT>

</HEAD>

<BODY BGCOLOR="white" onload="windowTitle();">
<HR>


<!-- ========= START OF TOP NAVBAR ======= -->
<A NAME="navbar_top"><!-- --></A>
<A HREF="#skip-navbar_top" title="Skip navigation links"></A>
<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
<TR>
<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
<A NAME="navbar_top_firstrow"><!-- --></A>
<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
  <TR ALIGN="center" VALIGN="top">
  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>
  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>
  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>
  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/MutationMention.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>
  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>
  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>
  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>
  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>
  </TR>
</TABLE>
</TD>
<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
</EM>
</TD>
</TR>

<TR>
<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
&nbsp;<A HREF="../../../../../de/hu/berlin/wbi/objects/HGVS.html" title="class in de.hu.berlin.wbi.objects"><B>PREV CLASS</B></A>&nbsp;
&nbsp;<A HREF="../../../../../de/hu/berlin/wbi/objects/MutationValidation.html" title="class in de.hu.berlin.wbi.objects"><B>NEXT CLASS</B></A></FONT></TD>
<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
  <A HREF="../../../../../index.html?de/hu/berlin/wbi/objects/MutationMention.html" target="_top"><B>FRAMES</B></A>  &nbsp;
&nbsp;<A HREF="MutationMention.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;
&nbsp;<SCRIPT type="text/javascript">
  <!--
  if(window==top) {
    document.writeln('<A HREF="../../../../../allclasses-noframe.html"><B>All Classes</B></A>');
  }
  //-->
</SCRIPT>
<NOSCRIPT>
  <A HREF="../../../../../allclasses-noframe.html"><B>All Classes</B></A>
</NOSCRIPT>


</FONT></TD>
</TR>
<TR>
<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>
<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>
</TR>
</TABLE>
<A NAME="skip-navbar_top"></A>
<!-- ========= END OF TOP NAVBAR ========= -->

<HR>
<!-- ======== START OF CLASS DATA ======== -->
<H2>
<FONT SIZE="-1">
de.hu.berlin.wbi.objects</FONT>
<BR>
Class MutationMention</H2>
<PRE>
<A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>
  <IMG SRC="../../../../../resources/inherit.gif" ALT="extended by "><B>de.hu.berlin.wbi.objects.MutationMention</B>
</PRE>
<DL>
<DT><B>Direct Known Subclasses:</B> <DD><A HREF="../../../../../de/hu/berlin/wbi/psb/MutationPSB.html" title="class in de.hu.berlin.wbi.psb">MutationPSB</A>, <A HREF="../../../../../de/hu/berlin/wbi/objects/MutationValidation.html" title="class in de.hu.berlin.wbi.objects">MutationValidation</A></DD>
</DL>
<HR>
<DL>
<DT><PRE>public class <B>MutationMention</B><DT>extends <A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></DL>
</PRE>

<P>
Class to represent a mutation mention found by an NER tool like 
 MutationFinder or SETH
<P>

<P>
<DL>
<DT><B>Author:</B></DT>
  <DD>Philippe Thomas</DD>
</DL>
<HR>

<P>

<!-- ======== CONSTRUCTOR SUMMARY ======== -->

<A NAME="constructor_summary"><!-- --></A>
<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
<B>Constructor Summary</B></FONT></TH>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD><CODE><B><A HREF="../../../../../de/hu/berlin/wbi/objects/MutationMention.html#MutationMention()">MutationMention</A></B>()</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD><CODE><B><A HREF="../../../../../de/hu/berlin/wbi/objects/MutationMention.html#MutationMention(de.hu.berlin.wbi.objects.EntityOffset, java.lang.String)">MutationMention</A></B>(<A HREF="../../../../../de/hu/berlin/wbi/objects/EntityOffset.html" title="class in de.hu.berlin.wbi.objects">EntityOffset</A>&nbsp;location,
                <A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;mutation)</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD><CODE><B><A HREF="../../../../../de/hu/berlin/wbi/objects/MutationMention.html#MutationMention(java.lang.String)">MutationMention</A></B>(<A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;mutation)</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Generates a Mutation object from a String like "A123T".</TD>
</TR>
</TABLE>
&nbsp;
<!-- ========== METHOD SUMMARY =========== -->

<A NAME="method_summary"><!-- --></A>
<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
<B>Method Summary</B></FONT></TH>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE>static&nbsp;<A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../../../de/hu/berlin/wbi/objects/dbSNPNormalized.html" title="class in de.hu.berlin.wbi.objects">dbSNPNormalized</A>&gt;</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../../../de/hu/berlin/wbi/objects/MutationMention.html#cleanResults(java.util.List)">cleanResults</A></B>(<A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../../../de/hu/berlin/wbi/objects/dbSNPNormalized.html" title="class in de.hu.berlin.wbi.objects">dbSNPNormalized</A>&gt;&nbsp;snpList)</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Sometimes one SNP mention can be normalized to the same dbSNP identifier 
 several times.</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE>&nbsp;<A HREF="../../../../../de/hu/berlin/wbi/objects/EntityOffset.html" title="class in de.hu.berlin.wbi.objects">EntityOffset</A></CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../../../de/hu/berlin/wbi/objects/MutationMention.html#getLocation()">getLocation</A></B>()</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Gets the location of the mutation</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE>&nbsp;<A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../../../de/hu/berlin/wbi/objects/MutationMention.html#getMutResidue()">getMutResidue</A></B>()</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Gets the residues.</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE>&nbsp;<A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../../../de/hu/berlin/wbi/objects/MutationMention.html#getPosition()">getPosition</A></B>()</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Gets the position.</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE>&nbsp;<A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../../../de/hu/berlin/wbi/objects/dbSNPNormalized.html" title="class in de.hu.berlin.wbi.objects">dbSNPNormalized</A>&gt;</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../../../de/hu/berlin/wbi/objects/MutationMention.html#getPossibledbSNPs(java.util.List, java.util.List)">getPossibledbSNPs</A></B>(<A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../../../de/hu/berlin/wbi/objects/dbSNP.html" title="class in de.hu.berlin.wbi.objects">dbSNP</A>&gt;&nbsp;candidates,
                  <A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../../../de/hu/berlin/wbi/objects/UniprotFeature.html" title="class in de.hu.berlin.wbi.objects">UniprotFeature</A>&gt;&nbsp;features)</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;This method evaluates if some of the <A HREF="../../../../../de/hu/berlin/wbi/objects/dbSNP.html" title="class in de.hu.berlin.wbi.objects"><CODE>dbSNP</CODE></A> provided in <b>candidates</b>
 actually equals the text-mined <CODE>Mutation</CODE></TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE>&nbsp;<A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../../../de/hu/berlin/wbi/objects/MutationMention.html#getWtResidue()">getWtResidue</A></B>()</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Gets the residue.</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE>&nbsp;boolean</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../../../de/hu/berlin/wbi/objects/MutationMention.html#isNsm()">isNsm</A></B>()</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Checks if is flag indicating if this SNP is possibly a NSM.</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE>static&nbsp;<A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/util/Map.html?is-external=true" title="class or interface in java.util">Map</A>&lt;<A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/Integer.html?is-external=true" title="class or interface in java.lang">Integer</A>,<A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../../../de/hu/berlin/wbi/objects/MutationMention.html" title="class in de.hu.berlin.wbi.objects">MutationMention</A>&gt;&gt;</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../../../de/hu/berlin/wbi/objects/MutationMention.html#readMutations(java.lang.String)">readMutations</A></B>(<A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;file)</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;This method loads Mutations from a file which are in the following format
 described in data/snps.txt (PMID\tWMutM\tstart\tstop)</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE>&nbsp;void</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../../../de/hu/berlin/wbi/objects/MutationMention.html#setLocation(de.hu.berlin.wbi.objects.EntityOffset)">setLocation</A></B>(<A HREF="../../../../../de/hu/berlin/wbi/objects/EntityOffset.html" title="class in de.hu.berlin.wbi.objects">EntityOffset</A>&nbsp;location)</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Sets the position of the mutation</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE>&nbsp;void</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../../../de/hu/berlin/wbi/objects/MutationMention.html#setMutResidue(java.lang.String)">setMutResidue</A></B>(<A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;mutResidue)</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Sets the residues.</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE>&nbsp;void</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../../../de/hu/berlin/wbi/objects/MutationMention.html#setPosition(java.lang.String)">setPosition</A></B>(<A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;position)</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Sets the position.</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE>&nbsp;void</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../../../de/hu/berlin/wbi/objects/MutationMention.html#setWtResidue(java.lang.String)">setWtResidue</A></B>(<A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;wtResidue)</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Sets the residue.</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE>&nbsp;<A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../../../de/hu/berlin/wbi/objects/MutationMention.html#toNormalized()">toNormalized</A></B>()</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE>&nbsp;<A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../../../de/hu/berlin/wbi/objects/MutationMention.html#toString()">toString</A></B>()</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(non-Javadoc)</TD>
</TR>
</TABLE>
&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
<TH ALIGN="left"><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD><CODE><A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/Object.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang">equals</A>, <A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/Object.html?is-external=true#hashCode()" title="class or interface in java.lang">hashCode</A>, <A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></CODE></TD>
</TR>
</TABLE>
&nbsp;
<P>

<!-- ========= CONSTRUCTOR DETAIL ======== -->

<A NAME="constructor_detail"><!-- --></A>
<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">
<B>Constructor Detail</B></FONT></TH>
</TR>
</TABLE>

<A NAME="MutationMention()"><!-- --></A><H3>
MutationMention</H3>
<PRE>
public <B>MutationMention</B>()</PRE>
<DL>
</DL>
<HR>

<A NAME="MutationMention(java.lang.String)"><!-- --></A><H3>
MutationMention</H3>
<PRE>
public <B>MutationMention</B>(<A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;mutation)</PRE>
<DL>
<DD>Generates a Mutation object from a String like "A123T".
<P>
<DL>
<DT><B>Parameters:</B><DD><CODE>mutation</CODE> - </DL>
</DL>
<HR>

<A NAME="MutationMention(de.hu.berlin.wbi.objects.EntityOffset, java.lang.String)"><!-- --></A><H3>
MutationMention</H3>
<PRE>
public <B>MutationMention</B>(<A HREF="../../../../../de/hu/berlin/wbi/objects/EntityOffset.html" title="class in de.hu.berlin.wbi.objects">EntityOffset</A>&nbsp;location,
                       <A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;mutation)</PRE>
<DL>
<DL>
<DT><B>Parameters:</B><DD><CODE>pmid</CODE> - <DD><CODE>location</CODE> - <DD><CODE>mutation</CODE> - </DL>
</DL>

<!-- ============ METHOD DETAIL ========== -->

<A NAME="method_detail"><!-- --></A>
<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">
<B>Method Detail</B></FONT></TH>
</TR>
</TABLE>

<A NAME="getPossibledbSNPs(java.util.List, java.util.List)"><!-- --></A><H3>
getPossibledbSNPs</H3>
<PRE>
public <A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../../../de/hu/berlin/wbi/objects/dbSNPNormalized.html" title="class in de.hu.berlin.wbi.objects">dbSNPNormalized</A>&gt; <B>getPossibledbSNPs</B>(<A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../../../de/hu/berlin/wbi/objects/dbSNP.html" title="class in de.hu.berlin.wbi.objects">dbSNP</A>&gt;&nbsp;candidates,
                                               <A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../../../de/hu/berlin/wbi/objects/UniprotFeature.html" title="class in de.hu.berlin.wbi.objects">UniprotFeature</A>&gt;&nbsp;features)</PRE>
<DL>
<DD>This method evaluates if some of the <A HREF="../../../../../de/hu/berlin/wbi/objects/dbSNP.html" title="class in de.hu.berlin.wbi.objects"><CODE>dbSNP</CODE></A> provided in <b>candidates</b>
 actually equals the text-mined <CODE>Mutation</CODE>
<P>
<DD><DL>
<DT><B>Parameters:</B><DD><CODE>candidates</CODE> - List of dbSNP-entries which might actually describe this
            NER-SNP
<DT><B>Returns:</B><DD>normalized mutations</DL>
</DD>
</DL>
<HR>

<A NAME="cleanResults(java.util.List)"><!-- --></A><H3>
cleanResults</H3>
<PRE>
public static <A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../../../de/hu/berlin/wbi/objects/dbSNPNormalized.html" title="class in de.hu.berlin.wbi.objects">dbSNPNormalized</A>&gt; <B>cleanResults</B>(<A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../../../de/hu/berlin/wbi/objects/dbSNPNormalized.html" title="class in de.hu.berlin.wbi.objects">dbSNPNormalized</A>&gt;&nbsp;snpList)</PRE>
<DL>
<DD>Sometimes one SNP mention can be normalized to the same dbSNP identifier 
 several times. As some information is stored redundant.
 Therefore we have to remove some duplicates from the list
<P>
<DD><DL>
<DT><B>Parameters:</B><DD><CODE>snpList</CODE> - 
<DT><B>Returns:</B><DD></DL>
</DD>
</DL>
<HR>

<A NAME="readMutations(java.lang.String)"><!-- --></A><H3>
readMutations</H3>
<PRE>
public static <A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/util/Map.html?is-external=true" title="class or interface in java.util">Map</A>&lt;<A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/Integer.html?is-external=true" title="class or interface in java.lang">Integer</A>,<A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../../../de/hu/berlin/wbi/objects/MutationMention.html" title="class in de.hu.berlin.wbi.objects">MutationMention</A>&gt;&gt; <B>readMutations</B>(<A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;file)
                                                        throws <A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/io/FileNotFoundException.html?is-external=true" title="class or interface in java.io">FileNotFoundException</A>,
                                                               <A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A></PRE>
<DL>
<DD>This method loads Mutations from a file which are in the following format
 described in data/snps.txt (PMID\tWMutM\tstart\tstop)
<P>
<DD><DL>
<DT><B>Parameters:</B><DD><CODE>file</CODE> - with mutations
<DT><B>Returns:</B><DD>Mao from pmids to all contained mutations
<DT><B>Throws:</B>
<DD><CODE><A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/io/FileNotFoundException.html?is-external=true" title="class or interface in java.io">FileNotFoundException</A></CODE>
<DD><CODE><A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A></CODE></DL>
</DD>
</DL>
<HR>

<A NAME="getLocation()"><!-- --></A><H3>
getLocation</H3>
<PRE>
public <A HREF="../../../../../de/hu/berlin/wbi/objects/EntityOffset.html" title="class in de.hu.berlin.wbi.objects">EntityOffset</A> <B>getLocation</B>()</PRE>
<DL>
<DD>Gets the location of the mutation
<P>
<DD><DL>

<DT><B>Returns:</B><DD>the location of the mutation</DL>
</DD>
</DL>
<HR>

<A NAME="setLocation(de.hu.berlin.wbi.objects.EntityOffset)"><!-- --></A><H3>
setLocation</H3>
<PRE>
public void <B>setLocation</B>(<A HREF="../../../../../de/hu/berlin/wbi/objects/EntityOffset.html" title="class in de.hu.berlin.wbi.objects">EntityOffset</A>&nbsp;location)</PRE>
<DL>
<DD>Sets the position of the mutation
<P>
<DD><DL>
<DT><B>Parameters:</B><DD><CODE>location</CODE> - the new position of the mutation</DL>
</DD>
</DL>
<HR>

<A NAME="getWtResidue()"><!-- --></A><H3>
getWtResidue</H3>
<PRE>
public <A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>getWtResidue</B>()</PRE>
<DL>
<DD>Gets the residue.
<P>
<DD><DL>

<DT><B>Returns:</B><DD>the residue</DL>
</DD>
</DL>
<HR>

<A NAME="setWtResidue(java.lang.String)"><!-- --></A><H3>
setWtResidue</H3>
<PRE>
public void <B>setWtResidue</B>(<A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;wtResidue)</PRE>
<DL>
<DD>Sets the residue.
<P>
<DD><DL>
<DT><B>Parameters:</B><DD><CODE>wtResidue</CODE> - the new residue</DL>
</DD>
</DL>
<HR>

<A NAME="getMutResidue()"><!-- --></A><H3>
getMutResidue</H3>
<PRE>
public <A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>getMutResidue</B>()</PRE>
<DL>
<DD>Gets the residues.
<P>
<DD><DL>

<DT><B>Returns:</B><DD>the residues</DL>
</DD>
</DL>
<HR>

<A NAME="setMutResidue(java.lang.String)"><!-- --></A><H3>
setMutResidue</H3>
<PRE>
public void <B>setMutResidue</B>(<A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;mutResidue)</PRE>
<DL>
<DD>Sets the residues.
<P>
<DD><DL>
<DT><B>Parameters:</B><DD><CODE>mutResidues</CODE> - the new residues</DL>
</DD>
</DL>
<HR>

<A NAME="getPosition()"><!-- --></A><H3>
getPosition</H3>
<PRE>
public <A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>getPosition</B>()</PRE>
<DL>
<DD>Gets the position.
<P>
<DD><DL>

<DT><B>Returns:</B><DD>the position</DL>
</DD>
</DL>
<HR>

<A NAME="setPosition(java.lang.String)"><!-- --></A><H3>
setPosition</H3>
<PRE>
public void <B>setPosition</B>(<A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;position)</PRE>
<DL>
<DD>Sets the position.
<P>
<DD><DL>
<DT><B>Parameters:</B><DD><CODE>position</CODE> - the new position</DL>
</DD>
</DL>
<HR>

<A NAME="toString()"><!-- --></A><H3>
toString</H3>
<PRE>
public <A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>toString</B>()</PRE>
<DL>
<DD>(non-Javadoc)
<P>
<DD><DL>
<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/Object.html?is-external=true#toString()" title="class or interface in java.lang">toString</A></CODE> in class <CODE><A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>
</DD>
<DD><DL>
<DT><B>See Also:</B><DD><A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/Object.html?is-external=true#toString()" title="class or interface in java.lang"><CODE>Object.toString()</CODE></A></DL>
</DD>
</DL>
<HR>

<A NAME="toNormalized()"><!-- --></A><H3>
toNormalized</H3>
<PRE>
public <A HREF="http://java.sun.com/j2se/1.5.0/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>toNormalized</B>()</PRE>
<DL>
<DD><DL>

<DT><B>Returns:</B><DD>SNP-description following the <wt><aa><mt> nomenclature</DL>
</DD>
</DL>
<HR>

<A NAME="isNsm()"><!-- --></A><H3>
isNsm</H3>
<PRE>
public boolean <B>isNsm</B>()</PRE>
<DL>
<DD>Checks if is flag indicating if this SNP is possibly a NSM.
<P>
<DD><DL>

<DT><B>Returns:</B><DD>the flag indicating if this SNP is possibly a NSM</DL>
</DD>
</DL>
<!-- ========= END OF CLASS DATA ========= -->
<HR>


<!-- ======= START OF BOTTOM NAVBAR ====== -->
<A NAME="navbar_bottom"><!-- --></A>
<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
<TR>
<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
<A NAME="navbar_bottom_firstrow"><!-- --></A>
<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
  <TR ALIGN="center" VALIGN="top">
  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>
  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>
  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>
  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/MutationMention.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>
  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>
  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>
  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>
  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>
  </TR>
</TABLE>
</TD>
<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
</EM>
</TD>
</TR>

<TR>
<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
&nbsp;<A HREF="../../../../../de/hu/berlin/wbi/objects/HGVS.html" title="class in de.hu.berlin.wbi.objects"><B>PREV CLASS</B></A>&nbsp;
&nbsp;<A HREF="../../../../../de/hu/berlin/wbi/objects/MutationValidation.html" title="class in de.hu.berlin.wbi.objects"><B>NEXT CLASS</B></A></FONT></TD>
<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
  <A HREF="../../../../../index.html?de/hu/berlin/wbi/objects/MutationMention.html" target="_top"><B>FRAMES</B></A>  &nbsp;
&nbsp;<A HREF="MutationMention.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;
&nbsp;<SCRIPT type="text/javascript">
  <!--
  if(window==top) {
    document.writeln('<A HREF="../../../../../allclasses-noframe.html"><B>All Classes</B></A>');
  }
  //-->
</SCRIPT>
<NOSCRIPT>
  <A HREF="../../../../../allclasses-noframe.html"><B>All Classes</B></A>
</NOSCRIPT>


</FONT></TD>
</TR>
<TR>
<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>
<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>
</TR>
</TABLE>
<A NAME="skip-navbar_bottom"></A>
<!-- ======== END OF BOTTOM NAVBAR ======= -->

<HR>

</BODY>
</HTML>
